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A Multi-scale CNN-CRF Framework for Environmental Microorganism Image Segmentation

In order to assist researchers to identify Environmental Microorganisms (EMs) effectively, a Multi-scale CNN-CRF (MSCC) framework for the EM image segmentation is proposed in this paper. There are two parts in this framework: The first is a novel pixel-level segmentation approach, using a newly introduced Convolutional Neural Network (CNN), namely "mU-Net-B3", with a dense Conditional Random Field (CRF) post-processing. The second is a VGG-16 based patch-level segmentation method with a novel "buffer" strategy, which further improves the segmentation quality of the details of the EMs. In the experiment, compared with the state-of-the-art methods on 420 EM images, the proposed MSCC method reduces the memory requirement from 355 MB to 103 MB, improves the overall evaluation indexes (Dice, Jaccard, Recall, Accuracy) from 85.24%, 77.42%, 82.27% and 96.76% to 87.13%, 79.74%, 87.12% and 96.91% respectively, and reduces the volume overlap error from 22.58% to 20.26%. Therefore, the MSCC method shows a big potential in the EM segmentation field.

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